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However, the full range of hierarchical indicators represented by a Linnaean classification (which species belong to which genera, which genera to families, families to orders, etc.) are usually also best held separately, as a different type of array – that o...

There are many cases in which analyses of different subsets of the samples or species are required. This can be easily achieved, without the need to create large numbers of separate datasheets, by temporarily selecting subsets from a single sheet, analysing th...

Dietary data on the gut contents of 7 marine fish species found in nearshore waters of the lower west coast of Western Australia are reported by Hourston M, Platell ME, Valesini FJ, Potter IC 2004, J Mar Biol Assoc UK 84: 805-817 and Schafer LN, Platell ME, Va...

File>Open>Filename: WA fish diets %vol, and examine the factors sheet with Edit>Factors. The samples form 7 groups (identified in the labels by A to G) which are the different predator species, three of which, B: Sillago schomburgkii (n = 10), E: Sillago bass...

Thus, with the WA fish diets %vol datasheet as the active window, highlight all columns except the three samples A9, B3 and B4. There are various ways of doing this. Clicking on a column label highlights that column (in light blue shading if the default Window...

When all except columns A9, B3 and B4 are highlighted, take Select>Highlighted. Alternatively, right click when over the data and a drop-down menu will appear, of operations from the Edit and Select menus, including Select highlighted. The matrix entries now h...

Though most Save operations are on whole workspaces, occasionally a data matrix needs to be saved externally, perhaps because it is needed in a different workspace or with other software. In order to protect against overwriting an original, external, data file...

The highlighting route to selection can be bypassed altogether using the other options on the Select main menu, Select>Samples and Select>Variables (and an example of the latter was seen in the previous section). Here, to select only those samples from the thr...

It is important to note the effect of this second selection on WA fish diets %vol; it produces a sheet of all samples from these three Sillago species. The prior exclusion of samples A9, B3 and B4 has been ignored – each new selection is a fresh operation on t...

It may sometimes be easier to use the sample numbers, here Select>Samples>•Sample numbers> 1,2,5,6,11,12,15,16, though this is more likely to be useful where such numerical lists are output in results (e.g. by the BEST routine, Section 13), and can be copied a...

Any of the options for selecting samples are also available for selecting variables, e.g. selecting by variable numbers or by levels of an indicator, the latter as seen in the example of the previous section, in which the Tasmanian copepods of ‘Undetermined ta...

There are, however, three other selection methods under Select>Variables that are specific to selecting species (or other taxon-type) variables, in which matrix entries are positive ‘amounts’ of that species (counts, biomass, area cover etc.). The idea of the ...

Looking ahead to Section 5, when the active window is a (triangular) resemblance matrix, selection can take place just as for a (rectangular) datasheet, by Select>Highlighted or Select>Samples>(•Sample numbers) or (•Factor levels). Another option is provided i...

How the data are treated, prior to computation of a resemblance matrix (e.g. similarities), can have an important influence on the final analysis, and such decisions often depend on the practical context rather than any statistical considerations. For example,...

Several of the routines in PRIMER 7 also incorporate a check box for sending summary statistics used in that routine to a further worksheet. Here, this results in a second sheet (probably named Data4), which is just a single column of totals across prey specie...

Pre-treatment>Standardise can also be used to standardise the matrix on the variables axis, e.g. to ensure that each species is given equal weight in any ensuing similarity calculation by making their totals across samples all add to 100, with (Standardise•Var...

Transformation is usually applied to all the entries in an assemblage matrix of counts, biomass, % area cover etc., in order to downweight the contributions of quantitatively dominant species to the similarities calculated between samples (see Chapters 2 and 9...

A major new feature in PRIMER 7 is the large number of additional plotting routines, one of the conceptually simplest but most powerful being Shade Plots, which are simple visualisations of the data matrix, with darker (or different colour) shades in each cell...

Transformations may be appropriate for environmental variables too, though usually for a different reason (e.g. in order to justify using Euclidean distance as a dissimilarity measure on normalised variables). However, these are usually selective transformati...

Temporarily deselect the Distance (as in Section 3), and run Plots>Draftsman Plot on the other 9 variables; also Plots>Histogram Plot (a new plotting feature in PRIMER 7). The latter leads to an example of another new feature, a Multi-plot (see Section 7), in ...